The two nations had volunteered to host the tournament in December after the original hosts - Cameroon - were stripped of the competition in light of Caf concerns about the country's infrastructure and security.
While Caf's near-unanimous decision to overlook South Africa as a potential Afcon destination may dent a few egos in southern Africa, it's a decision that ought to motivate the nation - and Bafana Bafana - rather than be viewed as a setback.
In truth, South Africa might have dodged a bullet.
While the country is capable of hosting any tournament, considering the infrastructure and sporting culture, it would have cost the country too much to put together a successful continental showpiece at such short notice.
South Africa needed at least R120 million, which the South African Football Association admitted that it didn't have, to put on the tournament, and therefore would have needed the government to step in.
They were reluctant to spend that amount of money on the tournament only six years after hosting it the last time, and were reportedly unwilling to offer any guarantees that they would offfer financial support.
Safa didn't even make an effort to promote their bid as much as they did for the Fifa World Cup and Afcon in 2010 and 2013 respectively beyond the submission of the documents to Caf. This is evidence that the federation didn't see the financial incentives in hosting the showpiece.
One of the main factors could have been the upcoming general election which is expected to take place in May this year. This would have shifted the focus more to football rather than politics, an unwanted scenario that they may have been keen to avoid.
While tournament hosting could have been an opportunity for the country to decrease the level of unemployment, especially among the youth, the lack of time between now and the kick off would have reduced this potential advantage.
The South African public showed less interest in hosting for the second time in such a short period of time, and this antipathy could also have led to poor attendance at the football venues.
Football fans in South Africa appear to be 'more interested' in attending local football than international matches, at least if Bafana Bafana's recent fixtures are anything to go by, and this could well have disuaded Caf from putting their weight behind the southern bid.
Bafana's recent underwhelming form has had a direct impact on interest in international matches and, therefore, on the appeal of a South African Afcon.
Perhaps this snub can come as a wake up call for the federation, and serve as a reminder of just how valuable a successful international team can be when it comes to promoting a nation and their football.
Hosting may be a shortcut to participation in major tournaments, but few know better than South Africa that it's no guarantee of success or even on-field improvement.
Bafana Bafana must strive to win matches and qualify for continental tournaments to be counted among the best, and not to rely only on hosting.
In 1996, South Africa stepped in to replace Kenya, while they took over from Libya in 2013. Did either occasion truly lead to sustained on-field improvement?
Losing the 2019 tournament need not be considered a setback for South Africa in any way. Instead, it can be a lesson and motivation for South Africa to work hard to return to the top again on the field, without relying on the decisions made in boardrooms and marketing houses.
Who knows, perhaps Stuart Baxter's team can make an impact in Egypt anyway, having qualified legitimately and not through the backdoor.
South Africa should congratulate Egypt for their success and go back to the drawing board to make sure that they avoid defeat away to Libya in March to book their place - on merit - among the continent's top teams.